4ZGN

Structure Cdc123 complexed with the C-terminal domain of eIF2gamma


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Cdc123, a Cell Cycle Regulator Needed for eIF2 Assembly, Is an ATP-Grasp Protein with Unique Features.

Panvert, M.Dubiez, E.Arnold, L.Perez, J.Mechulam, Y.Seufert, W.Schmitt, E.

(2015) Structure 23: 1596-1608

  • DOI: 10.1016/j.str.2015.06.014
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Eukaryotic initiation factor 2 (eIF2), a heterotrimeric guanosine triphosphatase, has a central role in protein biosynthesis by supplying methionylated initiator tRNA to the ribosomal translation initiation complex and by serving as a target for tran ...

    Eukaryotic initiation factor 2 (eIF2), a heterotrimeric guanosine triphosphatase, has a central role in protein biosynthesis by supplying methionylated initiator tRNA to the ribosomal translation initiation complex and by serving as a target for translational control in response to stress. Recent work identified a novel step indispensable for eIF2 function: assembly of eIF2 from its three subunits by the cell proliferation protein Cdc123. We report the first crystal structure of a Cdc123 representative, that from Schizosaccharomyces pombe, both isolated and bound to domain III of Saccharomyces cerevisiae eIF2γ. The structures show that Cdc123 resembles enzymes of the ATP-grasp family. Indeed, Cdc123 binds ATP-Mg(2+), and conserved residues contacting ATP-Mg(2+) are essential for Cdc123 to support eIF2 assembly and cell viability. A docking of eIF2αγ onto Cdc123, combined with genetic and biochemical experiments, allows us to propose a model explaining how Cdc123 participates in the biogenesis of eIF2 through facilitating assembly of eIF2γ to eIF2α.


    Organizational Affiliation

    Laboratoire de Biochimie, Ecole Polytechnique, CNRS, UMR7654, 91128 Palaiseau Cedex, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cell division cycle protein 123
A
338Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: cdc123
Find proteins for Q9P7N5 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9P7N5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 2 subunit gamma
B
118Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: GCD11 (TIF213)
Find proteins for P32481 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32481
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.195 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 74.260α = 90.00
b = 116.640β = 90.00
c = 132.580γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
BUSTERrefinement
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
CNRSFranceUMR7654
Ecole polytecFrance--

Revision History 

  • Version 1.0: 2015-09-30
    Type: Initial release